Molecular Mechanisms in the Repair of the Cyclobutane Dimer

Abstract

We investigate the molecular mechanism of the repair of the cyclobutane dimer radical anion in aqueous solution using ab initio MD simulations. Umbrella sampling is used to determine a two-dimensional free energy surface as a function of the C5-C5´ and C6-C6´ distances. The neutral dimer is unable to surmount a large free energy barrier for repair. Upon addition of an electron, the splitting of the C5-C5´ coordinate is virtually barrier less. Transition state theory predicts that the splitting of the C6-C6´ bond is complete on a ps timescale. The free energy surface suggests that the splitting of the two bonds is asynchronously concerted. Our work is the first to explicitly include the electronic degrees of freedom for both the cyclobutane dimer and the surrounding water pocket. The ab initio simulations show that at least 30% of the electron density is delocalized onto the surrounding solvent during the splitting process. Simulations on the neutral surface show that back electron transfer from the dimer is critical for the completion of splitting. To maximize splitting yield, the back electron transfer should occur beyond the transition state along the splitting coordinate.View Large Image | View Hi-Res Image | Download PowerPoint Slide